Starting phenix.real_space_refine
on Wed Mar  4 00:07:12 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/6xdg_22137/03_2026/6xdg_22137.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xdg_22137/03_2026/6xdg_22137.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xdg_22137/03_2026/6xdg_22137.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xdg_22137/03_2026/6xdg_22137.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xdg_22137/03_2026/6xdg_22137.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xdg_22137/03_2026/6xdg_22137.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1514 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    5058      2.51       5
     N    1320      2.21       5
     O    1594      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8004
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "E"
      Number of atoms: 1542
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
      Conformer: "B"
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
          bond proxies already assigned to first conformer: 1572
    Chain: "D"
      Number of atoms: 1640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1640
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202}
    Chain: "B"
      Number of atoms: 1603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1603
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1604
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1565
          Classifications: {'peptide': 211}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196}
    Chain: "F"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C1  MAN F   4 " occ=0.70
      ... (9 atoms not shown)
      pdb=" O6  MAN F   4 " occ=0.70
  Time building chain proxies: 2.30, per 1000 atoms: 0.29
  Number of scatterers: 8004
  At special positions: 0
  Unit cell: (72.25, 119.85, 150.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1594      8.00
     N    1320      7.00
     C    5058      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 134 " - pdb=" SG  CYS D 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 147 " - pdb=" SG  CYS B 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 147 " - pdb=" SG  CYS C 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 138 " - pdb=" SG  CYS A 197 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-6
      " BMA F   3 " - " MAN F   4 "
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG F   1 " - " ASN E 343 "
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 311.8 milliseconds
  

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1920

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 21 sheets defined
      8.8% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'E' and resid 337 through 343
    Processing helix  chain 'E' and resid 365 through 370
    Processing helix  chain 'E' and resid 383 through 389
      removed outlier: 3.753A  pdb=" N   ASP E 389 " --> pdb=" O   THR E 385 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 405 through 410
      removed outlier: 4.489A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 416 through 422
    Processing helix  chain 'D' and resid 121 through 128
    Processing helix  chain 'D' and resid 183 through 189
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 4.257A  pdb=" N   TYR B  32 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 91
    Processing helix  chain 'B' and resid 192 through 196
      removed outlier: 3.728A  pdb=" N   SER B 195 " --> pdb=" O   PRO B 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.823A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
    Processing helix  chain 'C' and resid 192 through 196
      removed outlier: 3.975A  pdb=" N   LEU C 196 " --> pdb=" O   SER C 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.798A  pdb=" N   GLN A 130 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 192
      removed outlier: 3.996A  pdb=" N   HIS A 192 " --> pdb=" O   GLN A 188 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.820A  pdb=" N   ASN E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   VAL E 395 " --> pdb=" O   ILE E 358 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE E 402 " --> pdb=" O   TYR E 508 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TRP E 436 " --> pdb=" O   ARG E 509 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 453
    Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.758A  pdb=" N   ASP D  70 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54
      removed outlier: 6.431A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   TYR D  49 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   LEU D  33 " --> pdb=" O   TYR D  49 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN D  34 " --> pdb=" O   GLN D  89 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLN D  89 " --> pdb=" O   ASN D  34 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR D  85 " --> pdb=" O   GLN D  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 118
      removed outlier: 3.513A  pdb=" N   SER D 114 " --> pdb=" O   ASN D 137 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   VAL D 133 " --> pdb=" O   PHE D 118 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   TYR D 173 " --> pdb=" O   ASN D 138 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   SER D 162 " --> pdb=" O   SER D 176 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 153 through 155
      removed outlier: 3.730A  pdb=" N   GLN D 155 " --> pdb=" O   TRP D 148 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   TRP D 148 " --> pdb=" O   GLN D 155 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LYS D 145 " --> pdb=" O   THR D 197 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR D 192 " --> pdb=" O   PHE D 209 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS D 207 " --> pdb=" O   CYS D 194 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.755A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   SER B  25 " --> pdb=" O   GLN B   3 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   TYR B  80 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   SER B  71 " --> pdb=" O   TYR B  80 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 60
      removed outlier: 6.739A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   TYR B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   MET B  34 " --> pdb=" O   TYR B  50 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASP B  99 " --> pdb=" O   TYR B  33 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 94
      removed outlier: 3.658A  pdb=" N   THR B 114 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 131
      removed outlier: 3.738A  pdb=" N   SER B 127 " --> pdb=" O   LYS B 150 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA B 143 " --> pdb=" O   VAL B 191 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER B 187 " --> pdb=" O   CYS B 147 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL B 149 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU B 185 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   SER B 184 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   ALA B 175 " --> pdb=" O   SER B 184 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   SER B 186 " --> pdb=" O   PHE B 173 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 158 through 161
      removed outlier: 3.717A  pdb=" N   THR B 158 " --> pdb=" O   ASN B 206 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.922A  pdb=" N   SER C  25 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU C  79 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 58 through 60
      removed outlier: 3.578A  pdb=" N   TYR C  59 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL C  50 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   VAL C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   MET C  34 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL C  93 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 127 through 131
      removed outlier: 4.472A  pdb=" N   SER C 127 " --> pdb=" O   LYS C 150 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LYS C 150 " --> pdb=" O   SER C 127 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU C 145 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER C 187 " --> pdb=" O   CYS C 147 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   TYR C 183 " --> pdb=" O   ASP C 151 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 205 through 206
      removed outlier: 3.515A  pdb=" N   VAL C 205 " --> pdb=" O   VAL C 214 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL C 214 " --> pdb=" O   VAL C 205 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'A' and resid 9 through 12
      removed outlier: 6.737A  pdb=" N   VAL A  10 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'A' and resid 17 through 23
    Processing sheet with id=AB9, first strand: chain 'A' and resid 47 through 51
      removed outlier: 5.444A  pdb=" N   LEU A  48 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   GLN A  39 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN A  40 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ASP A  87 " --> pdb=" O   GLN A  40 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   SER A  92 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL A 100 " --> pdb=" O   SER A  92 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 118 through 122
      removed outlier: 3.573A  pdb=" N   PHE A 122 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   SER A 141 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ALA A 178 " --> pdb=" O   SER A 141 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   SER A 169 " --> pdb=" O   ALA A 177 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 118 through 122
      removed outlier: 3.573A  pdb=" N   PHE A 122 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 158 through 159
      removed outlier: 3.565A  pdb=" N   TRP A 152 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN A 198 " --> pdb=" O   ALA A 151 " (cutoff:3.500A)

    209 hydrogen bonds defined for protein.
    531 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.11

  Time building geometry restraints manager: 0.86 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.35: 2535
        1.35 -     1.47: 2165
        1.47 -     1.59: 3460
        1.59 -     1.71: 0
        1.71 -     1.83: 39
  Bond restraints: 8199
  Sorted by residual:
  bond pdb=" C   PHE E 497 "
       pdb=" N   GLN E 498 "
    ideal  model  delta    sigma   weight residual
    1.329  1.293  0.035 1.60e-02 3.91e+03 4.86e+00
  bond pdb=" N   VAL B 176 "
       pdb=" CA  VAL B 176 "
    ideal  model  delta    sigma   weight residual
    1.459  1.441  0.018 1.25e-02 6.40e+03 2.15e+00
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.13e+00
  bond pdb=" C5  MAN F   4 "
       pdb=" O5  MAN F   4 "
    ideal  model  delta    sigma   weight residual
    1.418  1.444 -0.026 2.00e-02 2.50e+03 1.65e+00
  bond pdb=" CA  VAL D 110 "
       pdb=" CB  VAL D 110 "
    ideal  model  delta    sigma   weight residual
    1.553  1.544  0.009 7.40e-03 1.83e+04 1.44e+00
  ... (remaining 8194 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 10805
        1.62 -     3.24: 296
        3.24 -     4.86: 49
        4.86 -     6.49: 13
        6.49 -     8.11: 8
  Bond angle restraints: 11171
  Sorted by residual:
  angle pdb=" C   PHE E 497 "
        pdb=" N   GLN E 498 "
        pdb=" CA  GLN E 498 "
      ideal   model   delta    sigma   weight residual
     120.49  113.22    7.27 1.42e+00 4.96e-01 2.62e+01
  angle pdb=" C   TYR A  51 "
        pdb=" N   ASP A  52 "
        pdb=" CA  ASP A  52 "
      ideal   model   delta    sigma   weight residual
     121.54  129.53   -7.99 1.91e+00 2.74e-01 1.75e+01
  angle pdb=" C   VAL A  53 "
        pdb=" N   SER A  54 "
        pdb=" CA  SER A  54 "
      ideal   model   delta    sigma   weight residual
     120.23  127.04   -6.81 1.67e+00 3.59e-01 1.66e+01
  angle pdb=" N   SER C 100 "
        pdb=" CA  SER C 100 "
        pdb=" C   SER C 100 "
      ideal   model   delta    sigma   weight residual
     110.33  114.61   -4.28 1.29e+00 6.01e-01 1.10e+01
  angle pdb=" N   ASP A  52 "
        pdb=" CA  ASP A  52 "
        pdb=" C   ASP A  52 "
      ideal   model   delta    sigma   weight residual
     110.80  117.69   -6.89 2.13e+00 2.20e-01 1.05e+01
  ... (remaining 11166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.95: 4633
       21.95 -    43.89: 248
       43.89 -    65.84: 20
       65.84 -    87.78: 13
       87.78 -   109.73: 4
  Dihedral angle restraints: 4918
    sinusoidal: 1898
      harmonic: 3020
  Sorted by residual:
  dihedral pdb=" CA  CYS E 361 "
           pdb=" C   CYS E 361 "
           pdb=" N   VAL E 362 "
           pdb=" CA  VAL E 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.06   25.94     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  ASP A  52 "
           pdb=" C   ASP A  52 "
           pdb=" N   VAL A  53 "
           pdb=" CA  VAL A  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.16   25.84     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  ASP B 108 "
           pdb=" C   ASP B 108 "
           pdb=" N   TYR B 109 "
           pdb=" CA  TYR B 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.24  -25.76     0      5.00e+00 4.00e-02 2.66e+01
  ... (remaining 4915 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1150
       0.081 -    0.162: 109
       0.162 -    0.244: 0
       0.244 -    0.325: 2
       0.325 -    0.406: 1
  Chirality restraints: 1262
  Sorted by residual:
  chirality pdb=" C1  MAN F   4 "
            pdb=" O6  BMA F   3 "
            pdb=" C2  MAN F   4 "
            pdb=" O5  MAN F   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    1.99    0.41 2.00e-02 2.50e+03 4.12e+02
  chirality pdb=" C1  BMA F   3 "
            pdb=" O4  NAG F   2 "
            pdb=" C2  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-02 2.50e+03 1.62e+02
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.54    0.14 2.00e-02 2.50e+03 4.76e+01
  ... (remaining 1259 not shown)

  Planarity restraints: 1426
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 155 "    0.028 5.00e-02 4.00e+02   4.22e-02 2.84e+00
        pdb=" N   PRO C 156 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO C 156 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 156 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 110 "   -0.016 2.00e-02 2.50e+03   9.78e-03 2.39e+00
        pdb=" CG  TRP B 110 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 110 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 110 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 110 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 110 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 110 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 110 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 462 "    0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO E 463 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO E 463 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO E 463 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1423 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 317
        2.68 -     3.24: 8293
        3.24 -     3.79: 12628
        3.79 -     4.35: 16251
        4.35 -     4.90: 25992
  Nonbonded interactions: 63481
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 121 "
            pdb=" O   PRO B 130 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" O   PRO C 130 "
            pdb=" OG  SER A 125 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" O   TYR D 186 "
            pdb=" OH  TYR D 192 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" OG  SER D   7 "
            pdb=" OG1 THR D  22 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OD1 ASP A 142 "
            pdb=" NE2 GLN A 171 "
     model   vdw
     2.171 3.120
  ... (remaining 63476 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 1 through 10 or resid 12 or resid 14 through 15 or resid 1 \ 
7 through 30 or resid 32 or resid 34 or resid 36 or resid 38 through 48 or resid \ 
 51 or resid 53 or resid 55 through 56 or resid 59 through 74 or resid 76 or res \ 
id 79 through 87 or resid 89 through 97 or resid 109 through 220))
  selection = (chain 'C' and (resid 1 through 10 or resid 12 or resid 14 through 15 or resid 1 \ 
7 through 30 or resid 32 or resid 34 or resid 36 or resid 38 through 48 or resid \ 
 51 or resid 53 or resid 55 through 56 or resid 59 through 74 or resid 76 or res \ 
id 79 through 87 or resid 89 through 97 or resid 109 through 220))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.790
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8213  Z= 0.210
  Angle     :  0.897  46.634  11203  Z= 0.419
  Chirality :  0.046   0.406   1262
  Planarity :  0.004   0.042   1425
  Dihedral  : 13.904 109.730   2968
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 19.30
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  9.82 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.87 (0.23), residues: 1030
  helix: -3.19 (0.52), residues: 48
  sheet: -2.30 (0.24), residues: 377
  loop : -2.77 (0.23), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  98 
 TYR   0.014   0.001   TYR E 495 
 PHE   0.013   0.002   PHE C  68 
 TRP   0.025   0.002   TRP B 110 
 HIS   0.003   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 8199)
  covalent geometry    : angle       0.70083 (11171)
  SS BOND              : bond        0.00292 (   10)
  SS BOND              : angle       1.07632 (   20)
  hydrogen bonds       : bond        0.33702 (  205)
  hydrogen bonds       : angle      11.45147 (  531)
  link_ALPHA1-6        : bond        0.06424 (    1)
  link_ALPHA1-6        : angle      12.26008 (    3)
  link_BETA1-4         : bond        0.06496 (    2)
  link_BETA1-4         : angle      22.48496 (    6)
  link_NAG-ASN         : bond        0.00253 (    1)
  link_NAG-ASN         : angle       2.27813 (    3)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  340 GLU cc_start: 0.9165 (pp20) cc_final: 0.8961 (pp20)
REVERT: E  386 LYS cc_start: 0.9132 (mptt) cc_final: 0.8812 (tptt)
REVERT: E  406 GLU cc_start: 0.9390 (mt-10) cc_final: 0.8665 (mp0)
REVERT: E  432 CYS cc_start: 0.7903 (t) cc_final: 0.7527 (m)
REVERT: E  465 GLU cc_start: 0.7124 (tt0) cc_final: 0.6806 (tt0)
REVERT: E  471 GLU cc_start: 0.8883 (tp30) cc_final: 0.8616 (tm-30)
REVERT: D   93 ASN cc_start: 0.8525 (m110) cc_final: 0.8140 (t0)
REVERT: D  105 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8111 (pt0)
REVERT: D  142 ARG cc_start: 0.8989 (tmt170) cc_final: 0.8743 (ttp80)
REVERT: D  187 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8841 (mm-30)
REVERT: B  199 GLN cc_start: 0.8327 (mt0) cc_final: 0.8068 (tp40)
REVERT: B  216 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8728 (ttpp)
REVERT: C    4 LEU cc_start: 0.8118 (mt) cc_final: 0.7853 (mt)
REVERT: A   49 MET cc_start: 0.8318 (mmm) cc_final: 0.7818 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1247
  time to fit residues: 20.5485
Evaluate side-chains
  87 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    8.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 388 ASN
E 474 GLN
E 487 ASN
D  38 GLN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  93 ASN
** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 189 HIS
D 210 ASN
B  82 GLN
B 178 GLN
B 207 HIS
C   1 GLN
C 162 ASN
C 199 GLN
C 204 ASN
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  81 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.080753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.054052 restraints weight = 45958.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.056844 restraints weight = 19167.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.058581 restraints weight = 11338.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.059679 restraints weight = 8113.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.060315 restraints weight = 6539.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3227
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3227 r_free = 0.3227    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3227 r_free = 0.3227    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3227
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8213  Z= 0.213
  Angle     :  0.763  11.043  11203  Z= 0.390
  Chirality :  0.047   0.167   1262
  Planarity :  0.005   0.072   1425
  Dihedral  :  8.669  87.526   1210
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.94 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.47 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.24), residues: 1030
  helix: -2.47 (0.51), residues: 60
  sheet: -1.56 (0.26), residues: 370
  loop : -2.43 (0.23), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  98 
 TYR   0.018   0.002   TYR B 201 
 PHE   0.021   0.002   PHE E 400 
 TRP   0.018   0.002   TRP B 110 
 HIS   0.004   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 8199)
  covalent geometry    : angle       0.75312 (11171)
  SS BOND              : bond        0.00419 (   10)
  SS BOND              : angle       1.86542 (   20)
  hydrogen bonds       : bond        0.05295 (  205)
  hydrogen bonds       : angle       8.30917 (  531)
  link_ALPHA1-6        : bond        0.01966 (    1)
  link_ALPHA1-6        : angle       1.54709 (    3)
  link_BETA1-4         : bond        0.01154 (    2)
  link_BETA1-4         : angle       4.17524 (    6)
  link_NAG-ASN         : bond        0.00018 (    1)
  link_NAG-ASN         : angle       1.32751 (    3)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.9150 (mptt) cc_final: 0.8806 (tptt)
REVERT: E  406 GLU cc_start: 0.9410 (mt-10) cc_final: 0.8602 (mp0)
REVERT: E  465 GLU cc_start: 0.7386 (tt0) cc_final: 0.7024 (tt0)
REVERT: D   93 ASN cc_start: 0.8820 (m-40) cc_final: 0.8352 (t0)
REVERT: D  105 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8153 (pt0)
REVERT: D  142 ARG cc_start: 0.8902 (tmt170) cc_final: 0.8509 (ttp80)
REVERT: D  187 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8709 (mm-30)
REVERT: B   32 TYR cc_start: 0.8411 (m-80) cc_final: 0.8090 (m-80)
REVERT: B  199 GLN cc_start: 0.8446 (mt0) cc_final: 0.8134 (tp40)
REVERT: B  216 LYS cc_start: 0.9239 (ttmm) cc_final: 0.8785 (ttpp)
REVERT: B  217 LYS cc_start: 0.8801 (tppp) cc_final: 0.8547 (tptp)
REVERT: C    4 LEU cc_start: 0.8429 (mt) cc_final: 0.8201 (mt)
REVERT: A   38 TYR cc_start: 0.7998 (m-80) cc_final: 0.7787 (m-80)
REVERT: A   49 MET cc_start: 0.8422 (mmm) cc_final: 0.7871 (mmm)
  outliers start: 11
  outliers final: 6
  residues processed: 117
  average time/residue: 0.1172
  time to fit residues: 17.2963
Evaluate side-chains
  91 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  515 PHE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain A residue   35 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 57 optimal weight:    0.7980
   chunk 76 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 189 HIS
B  82 GLN
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 198 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.080624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.052804 restraints weight = 66835.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.056063 restraints weight = 23325.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.058042 restraints weight = 12770.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.059275 restraints weight = 8721.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.060001 restraints weight = 6818.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8213  Z= 0.198
  Angle     :  0.712   9.633  11203  Z= 0.363
  Chirality :  0.045   0.160   1262
  Planarity :  0.005   0.054   1425
  Dihedral  :  7.816  74.449   1210
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.36 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.25 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.69 (0.25), residues: 1030
  helix: -2.28 (0.54), residues: 61
  sheet: -1.19 (0.27), residues: 380
  loop : -2.19 (0.24), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  98 
 TYR   0.013   0.002   TYR E 495 
 PHE   0.015   0.002   PHE E 400 
 TRP   0.015   0.002   TRP B 110 
 HIS   0.006   0.001   HIS D 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 8199)
  covalent geometry    : angle       0.70269 (11171)
  SS BOND              : bond        0.00361 (   10)
  SS BOND              : angle       1.68547 (   20)
  hydrogen bonds       : bond        0.04468 (  205)
  hydrogen bonds       : angle       7.73086 (  531)
  link_ALPHA1-6        : bond        0.00988 (    1)
  link_ALPHA1-6        : angle       2.11468 (    3)
  link_BETA1-4         : bond        0.00616 (    2)
  link_BETA1-4         : angle       4.03576 (    6)
  link_NAG-ASN         : bond        0.00017 (    1)
  link_NAG-ASN         : angle       1.05884 (    3)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.9128 (mptt) cc_final: 0.8816 (tptt)
REVERT: E  406 GLU cc_start: 0.9378 (mt-10) cc_final: 0.8642 (mp0)
REVERT: E  424 LYS cc_start: 0.8976 (tptm) cc_final: 0.8737 (mptm)
REVERT: E  465 GLU cc_start: 0.7386 (tt0) cc_final: 0.7051 (tt0)
REVERT: D   93 ASN cc_start: 0.8841 (m-40) cc_final: 0.8378 (t0)
REVERT: D  105 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8119 (pt0)
REVERT: D  142 ARG cc_start: 0.8891 (tmt170) cc_final: 0.8555 (ttp80)
REVERT: D  187 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8696 (mm-30)
REVERT: B  199 GLN cc_start: 0.8449 (mt0) cc_final: 0.8112 (tp40)
REVERT: B  216 LYS cc_start: 0.9263 (ttmm) cc_final: 0.8937 (ttpp)
REVERT: C  147 CYS cc_start: 0.7684 (p) cc_final: 0.6420 (m)
REVERT: A   38 TYR cc_start: 0.8141 (m-80) cc_final: 0.7769 (m-80)
REVERT: A   49 MET cc_start: 0.8438 (mmm) cc_final: 0.7919 (mmm)
  outliers start: 25
  outliers final: 18
  residues processed: 121
  average time/residue: 0.1110
  time to fit residues: 17.2600
Evaluate side-chains
  99 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain E residue  515 PHE
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   98 ARG
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue   35 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 100 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 189 HIS
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.081102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.054519 restraints weight = 44072.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.057331 restraints weight = 17935.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.059074 restraints weight = 10466.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.060127 restraints weight = 7430.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.060747 restraints weight = 6003.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8213  Z= 0.179
  Angle     :  0.702   9.982  11203  Z= 0.357
  Chirality :  0.045   0.200   1262
  Planarity :  0.005   0.071   1425
  Dihedral  :  7.209  62.973   1210
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.45 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.60 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.26), residues: 1030
  helix: -2.16 (0.59), residues: 55
  sheet: -0.96 (0.27), residues: 381
  loop : -2.00 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  98 
 TYR   0.025   0.002   TYR E 495 
 PHE   0.025   0.002   PHE E 497 
 TRP   0.012   0.002   TRP B 110 
 HIS   0.004   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8199)
  covalent geometry    : angle       0.69300 (11171)
  SS BOND              : bond        0.00712 (   10)
  SS BOND              : angle       1.84790 (   20)
  hydrogen bonds       : bond        0.03769 (  205)
  hydrogen bonds       : angle       7.30992 (  531)
  link_ALPHA1-6        : bond        0.01221 (    1)
  link_ALPHA1-6        : angle       2.01763 (    3)
  link_BETA1-4         : bond        0.00445 (    2)
  link_BETA1-4         : angle       3.60079 (    6)
  link_NAG-ASN         : bond        0.00150 (    1)
  link_NAG-ASN         : angle       0.95320 (    3)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.9107 (mptt) cc_final: 0.8789 (tptt)
REVERT: E  406 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8553 (mp0)
REVERT: E  424 LYS cc_start: 0.8912 (tptm) cc_final: 0.8667 (mptm)
REVERT: E  465 GLU cc_start: 0.7343 (tt0) cc_final: 0.6981 (tt0)
REVERT: E  471 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8378 (tm-30)
REVERT: D    4 MET cc_start: 0.8148 (mmm) cc_final: 0.7886 (mmm)
REVERT: D   93 ASN cc_start: 0.8808 (m-40) cc_final: 0.8340 (t0)
REVERT: D  105 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8123 (pt0)
REVERT: D  142 ARG cc_start: 0.8852 (tmt170) cc_final: 0.8339 (ttp80)
REVERT: B  199 GLN cc_start: 0.8554 (mt0) cc_final: 0.8269 (tp40)
REVERT: B  206 ASN cc_start: 0.7135 (t0) cc_final: 0.6782 (t0)
REVERT: B  216 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8167 (ttpp)
REVERT: C  147 CYS cc_start: 0.7737 (p) cc_final: 0.6686 (m)
REVERT: A   38 TYR cc_start: 0.8135 (m-80) cc_final: 0.7732 (m-80)
REVERT: A   49 MET cc_start: 0.8407 (mmm) cc_final: 0.7878 (mmm)
  outliers start: 25
  outliers final: 18
  residues processed: 115
  average time/residue: 0.1130
  time to fit residues: 16.5782
Evaluate side-chains
  106 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain E residue  515 PHE
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   98 ARG
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue   35 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 93 optimal weight:   30.0000
   chunk 36 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 100 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 46 optimal weight:    0.1980
   chunk 60 optimal weight:    4.9990
   chunk 96 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.081402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.054224 restraints weight = 49894.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.057290 restraints weight = 19180.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.059163 restraints weight = 10802.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.060267 restraints weight = 7466.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 61)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.060982 restraints weight = 5946.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8213  Z= 0.133
  Angle     :  0.675  10.664  11203  Z= 0.339
  Chirality :  0.045   0.188   1262
  Planarity :  0.005   0.050   1425
  Dihedral  :  6.516  50.591   1210
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.26 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.61 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.26), residues: 1030
  helix: -2.04 (0.58), residues: 55
  sheet: -0.84 (0.27), residues: 384
  loop : -1.82 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  98 
 TYR   0.022   0.001   TYR E 495 
 PHE   0.040   0.002   PHE E 497 
 TRP   0.010   0.001   TRP B 110 
 HIS   0.003   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8199)
  covalent geometry    : angle       0.66858 (11171)
  SS BOND              : bond        0.00466 (   10)
  SS BOND              : angle       1.50151 (   20)
  hydrogen bonds       : bond        0.03276 (  205)
  hydrogen bonds       : angle       7.02130 (  531)
  link_ALPHA1-6        : bond        0.01125 (    1)
  link_ALPHA1-6        : angle       1.87276 (    3)
  link_BETA1-4         : bond        0.00657 (    2)
  link_BETA1-4         : angle       3.10873 (    6)
  link_NAG-ASN         : bond        0.00309 (    1)
  link_NAG-ASN         : angle       0.86232 (    3)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.9337 (mt-10) cc_final: 0.8565 (mp0)
REVERT: E  424 LYS cc_start: 0.8896 (tptm) cc_final: 0.8662 (mptm)
REVERT: E  465 GLU cc_start: 0.7294 (tt0) cc_final: 0.7034 (tt0)
REVERT: E  468 ILE cc_start: 0.9288 (pt) cc_final: 0.9010 (tp)
REVERT: D   93 ASN cc_start: 0.8706 (m-40) cc_final: 0.8267 (t0)
REVERT: D  105 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8089 (pt0)
REVERT: D  142 ARG cc_start: 0.8748 (tmt170) cc_final: 0.8267 (ttp80)
REVERT: D  187 GLU cc_start: 0.9529 (tp30) cc_final: 0.9328 (pt0)
REVERT: B   43 LYS cc_start: 0.8656 (mptt) cc_final: 0.8448 (mptt)
REVERT: B   62 ASP cc_start: 0.8492 (t0) cc_final: 0.8195 (t0)
REVERT: B  199 GLN cc_start: 0.8539 (mt0) cc_final: 0.8228 (tp40)
REVERT: B  213 LYS cc_start: 0.9330 (mtpt) cc_final: 0.8883 (tptt)
REVERT: B  216 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8210 (ttpp)
REVERT: C  147 CYS cc_start: 0.7699 (p) cc_final: 0.6767 (m)
REVERT: A   38 TYR cc_start: 0.7961 (m-80) cc_final: 0.7589 (m-80)
REVERT: A   49 MET cc_start: 0.8426 (mmm) cc_final: 0.7879 (mmm)
  outliers start: 22
  outliers final: 17
  residues processed: 117
  average time/residue: 0.1037
  time to fit residues: 15.8751
Evaluate side-chains
  103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain E residue  515 PHE
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  140 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 40 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 25 optimal weight:   20.0000
   chunk 22 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 20 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    2.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 354 ASN
E 360 ASN
E 481 ASN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.080477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.052614 restraints weight = 65106.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.055875 restraints weight = 22660.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.057888 restraints weight = 12257.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.059121 restraints weight = 8248.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.059851 restraints weight = 6394.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8213  Z= 0.178
  Angle     :  0.678  10.871  11203  Z= 0.345
  Chirality :  0.044   0.185   1262
  Planarity :  0.005   0.074   1425
  Dihedral  :  6.073  39.667   1210
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.75 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 17.28 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.26), residues: 1030
  helix: -1.81 (0.56), residues: 61
  sheet: -0.77 (0.28), residues: 378
  loop : -1.74 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  98 
 TYR   0.038   0.002   TYR E 495 
 PHE   0.043   0.002   PHE E 497 
 TRP   0.011   0.002   TRP A 152 
 HIS   0.003   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8199)
  covalent geometry    : angle       0.67173 (11171)
  SS BOND              : bond        0.00417 (   10)
  SS BOND              : angle       1.42276 (   20)
  hydrogen bonds       : bond        0.03326 (  205)
  hydrogen bonds       : angle       6.87930 (  531)
  link_ALPHA1-6        : bond        0.01361 (    1)
  link_ALPHA1-6        : angle       1.77758 (    3)
  link_BETA1-4         : bond        0.00604 (    2)
  link_BETA1-4         : angle       2.94964 (    6)
  link_NAG-ASN         : bond        0.00055 (    1)
  link_NAG-ASN         : angle       1.23448 (    3)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  392 PHE cc_start: 0.8059 (m-80) cc_final: 0.7857 (m-80)
REVERT: E  406 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8594 (mp0)
REVERT: E  465 GLU cc_start: 0.7254 (tt0) cc_final: 0.7022 (tt0)
REVERT: E  468 ILE cc_start: 0.9266 (pt) cc_final: 0.8984 (tp)
REVERT: D   93 ASN cc_start: 0.8713 (m-40) cc_final: 0.8249 (t0)
REVERT: D  105 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7761 (mp0)
REVERT: D  142 ARG cc_start: 0.8725 (tmt170) cc_final: 0.8206 (ttp80)
REVERT: B   13 LYS cc_start: 0.9093 (mmmm) cc_final: 0.8477 (tptp)
REVERT: B   43 LYS cc_start: 0.8647 (mptt) cc_final: 0.8398 (mptt)
REVERT: B   62 ASP cc_start: 0.8556 (t0) cc_final: 0.8256 (t0)
REVERT: B  199 GLN cc_start: 0.8537 (mt0) cc_final: 0.8230 (tp40)
REVERT: B  213 LYS cc_start: 0.9350 (mtpt) cc_final: 0.8864 (tptt)
REVERT: B  216 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8189 (ttpp)
REVERT: C  129 PHE cc_start: 0.8261 (m-10) cc_final: 0.8027 (m-10)
REVERT: C  147 CYS cc_start: 0.7725 (p) cc_final: 0.6812 (m)
REVERT: A   38 TYR cc_start: 0.8128 (m-80) cc_final: 0.7638 (m-80)
REVERT: A   49 MET cc_start: 0.8382 (mmm) cc_final: 0.7848 (mmm)
  outliers start: 29
  outliers final: 25
  residues processed: 107
  average time/residue: 0.1013
  time to fit residues: 14.1471
Evaluate side-chains
  108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain E residue  515 PHE
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   98 ARG
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  165 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   chunk 73 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 96 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    2.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.079465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.051889 restraints weight = 60411.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.055006 restraints weight = 22077.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.056944 restraints weight = 12177.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.058099 restraints weight = 8288.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 61)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.058858 restraints weight = 6478.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8213  Z= 0.211
  Angle     :  0.693  10.722  11203  Z= 0.356
  Chirality :  0.045   0.181   1262
  Planarity :  0.005   0.053   1425
  Dihedral  :  5.837  46.795   1210
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.94 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 17.28 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.27), residues: 1030
  helix: -1.90 (0.55), residues: 63
  sheet: -0.85 (0.27), residues: 387
  loop : -1.71 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  98 
 TYR   0.028   0.002   TYR E 495 
 PHE   0.050   0.002   PHE E 497 
 TRP   0.014   0.002   TRP B 110 
 HIS   0.003   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 8199)
  covalent geometry    : angle       0.68744 (11171)
  SS BOND              : bond        0.00369 (   10)
  SS BOND              : angle       1.37490 (   20)
  hydrogen bonds       : bond        0.03505 (  205)
  hydrogen bonds       : angle       6.82620 (  531)
  link_ALPHA1-6        : bond        0.01139 (    1)
  link_ALPHA1-6        : angle       1.28515 (    3)
  link_BETA1-4         : bond        0.00540 (    2)
  link_BETA1-4         : angle       2.77886 (    6)
  link_NAG-ASN         : bond        0.00060 (    1)
  link_NAG-ASN         : angle       1.46218 (    3)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 82
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.9079 (mptt) cc_final: 0.8766 (tptt)
REVERT: E  406 GLU cc_start: 0.9398 (mt-10) cc_final: 0.8630 (mp0)
REVERT: E  465 GLU cc_start: 0.7217 (tt0) cc_final: 0.7009 (tt0)
REVERT: D    4 MET cc_start: 0.8187 (mmm) cc_final: 0.7886 (mmm)
REVERT: D   93 ASN cc_start: 0.8761 (m-40) cc_final: 0.8289 (t0)
REVERT: D  105 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7739 (mp0)
REVERT: D  142 ARG cc_start: 0.8730 (tmt170) cc_final: 0.8208 (ttp80)
REVERT: B   62 ASP cc_start: 0.8533 (t0) cc_final: 0.8239 (t0)
REVERT: B   76 LYS cc_start: 0.9617 (mtmm) cc_final: 0.9387 (mtmm)
REVERT: B  199 GLN cc_start: 0.8507 (mt0) cc_final: 0.8181 (tp40)
REVERT: B  213 LYS cc_start: 0.9332 (mtpt) cc_final: 0.8847 (tptt)
REVERT: B  216 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8230 (ttpp)
REVERT: C  129 PHE cc_start: 0.8261 (m-10) cc_final: 0.7993 (m-10)
REVERT: C  147 CYS cc_start: 0.7711 (p) cc_final: 0.6993 (m)
REVERT: A   38 TYR cc_start: 0.8142 (m-80) cc_final: 0.7597 (m-80)
REVERT: A   49 MET cc_start: 0.8374 (mmm) cc_final: 0.7851 (mmm)
  outliers start: 32
  outliers final: 27
  residues processed: 108
  average time/residue: 0.1074
  time to fit residues: 15.0589
Evaluate side-chains
  102 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain E residue  515 PHE
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   98 ARG
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  140 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0030
   chunk 5 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 71 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0060
   chunk 73 optimal weight:    8.9990
   overall best weight:    0.5808

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D   6 GLN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 204 ASN
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.083763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.057092 restraints weight = 44257.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.060065 restraints weight = 17951.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.061910 restraints weight = 10385.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.062979 restraints weight = 7309.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.063669 restraints weight = 5879.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8213  Z= 0.118
  Angle     :  0.675  10.923  11203  Z= 0.341
  Chirality :  0.044   0.177   1262
  Planarity :  0.005   0.077   1425
  Dihedral  :  5.544  59.287   1210
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.29 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 19.53 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.27), residues: 1030
  helix: -1.80 (0.57), residues: 64
  sheet: -0.61 (0.28), residues: 386
  loop : -1.51 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  19 
 TYR   0.025   0.001   TYR A  34 
 PHE   0.031   0.001   PHE E 497 
 TRP   0.016   0.002   TRP B 161 
 HIS   0.004   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8199)
  covalent geometry    : angle       0.67148 (11171)
  SS BOND              : bond        0.00452 (   10)
  SS BOND              : angle       1.17674 (   20)
  hydrogen bonds       : bond        0.02910 (  205)
  hydrogen bonds       : angle       6.48858 (  531)
  link_ALPHA1-6        : bond        0.00835 (    1)
  link_ALPHA1-6        : angle       1.38864 (    3)
  link_BETA1-4         : bond        0.00721 (    2)
  link_BETA1-4         : angle       2.18771 (    6)
  link_NAG-ASN         : bond        0.00375 (    1)
  link_NAG-ASN         : angle       1.04360 (    3)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8580 (mp0)
REVERT: E  468 ILE cc_start: 0.9276 (pt) cc_final: 0.9002 (tp)
REVERT: D   93 ASN cc_start: 0.8674 (m-40) cc_final: 0.8256 (t0)
REVERT: D  105 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7717 (mp0)
REVERT: D  142 ARG cc_start: 0.8602 (tmt170) cc_final: 0.8063 (ttp80)
REVERT: D  187 GLU cc_start: 0.9552 (tp30) cc_final: 0.9258 (pt0)
REVERT: B  199 GLN cc_start: 0.8472 (mt0) cc_final: 0.8114 (tm-30)
REVERT: B  216 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8116 (ttpp)
REVERT: C  129 PHE cc_start: 0.8234 (m-10) cc_final: 0.7990 (m-10)
REVERT: C  147 CYS cc_start: 0.7564 (p) cc_final: 0.6826 (m)
REVERT: A   38 TYR cc_start: 0.7795 (m-80) cc_final: 0.7412 (m-80)
REVERT: A   49 MET cc_start: 0.8354 (mmm) cc_final: 0.7810 (mmm)
  outliers start: 23
  outliers final: 16
  residues processed: 112
  average time/residue: 0.1036
  time to fit residues: 15.2496
Evaluate side-chains
  103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain E residue  515 PHE
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  214 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   chunk 4 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    0.1980
   overall best weight:    2.8386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.081098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.054213 restraints weight = 52400.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.057171 restraints weight = 20594.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.059000 restraints weight = 11846.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.060075 restraints weight = 8325.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.060764 restraints weight = 6700.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8213  Z= 0.201
  Angle     :  0.695  10.664  11203  Z= 0.356
  Chirality :  0.044   0.189   1262
  Planarity :  0.005   0.073   1425
  Dihedral  :  5.669  59.479   1210
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.07 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.65 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.27), residues: 1030
  helix: -1.79 (0.56), residues: 64
  sheet: -0.77 (0.27), residues: 397
  loop : -1.54 (0.27), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  18 
 TYR   0.028   0.002   TYR A 176 
 PHE   0.040   0.002   PHE E 497 
 TRP   0.013   0.002   TRP A  99 
 HIS   0.003   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 8199)
  covalent geometry    : angle       0.69157 (11171)
  SS BOND              : bond        0.00417 (   10)
  SS BOND              : angle       1.22856 (   20)
  hydrogen bonds       : bond        0.03374 (  205)
  hydrogen bonds       : angle       6.54025 (  531)
  link_ALPHA1-6        : bond        0.00701 (    1)
  link_ALPHA1-6        : angle       1.15130 (    3)
  link_BETA1-4         : bond        0.00615 (    2)
  link_BETA1-4         : angle       2.31034 (    6)
  link_NAG-ASN         : bond        0.00102 (    1)
  link_NAG-ASN         : angle       1.61432 (    3)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  338 PHE cc_start: 0.9169 (m-80) cc_final: 0.8908 (m-80)
REVERT: E  406 GLU cc_start: 0.9373 (mt-10) cc_final: 0.8638 (mp0)
REVERT: E  465 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7561 (tt0)
REVERT: E  468 ILE cc_start: 0.9280 (pt) cc_final: 0.9005 (tp)
REVERT: D   18 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7989 (ttp80)
REVERT: D   93 ASN cc_start: 0.8786 (m-40) cc_final: 0.8344 (t0)
REVERT: D  105 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7725 (mp0)
REVERT: D  142 ARG cc_start: 0.8681 (tmt170) cc_final: 0.8123 (ttp80)
REVERT: B   62 ASP cc_start: 0.8461 (t0) cc_final: 0.8208 (t0)
REVERT: B  199 GLN cc_start: 0.8436 (mt0) cc_final: 0.8145 (tp40)
REVERT: B  213 LYS cc_start: 0.9335 (mtpt) cc_final: 0.8854 (tptt)
REVERT: B  216 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8216 (ttpp)
REVERT: C   68 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8413 (m-10)
REVERT: C  147 CYS cc_start: 0.7911 (p) cc_final: 0.7036 (m)
REVERT: A   38 TYR cc_start: 0.8083 (m-80) cc_final: 0.7467 (m-80)
REVERT: A   49 MET cc_start: 0.8387 (mmm) cc_final: 0.7837 (mmm)
  outliers start: 23
  outliers final: 19
  residues processed: 106
  average time/residue: 0.0962
  time to fit residues: 13.5681
Evaluate side-chains
  103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain E residue  515 PHE
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain C residue   68 PHE
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue  101 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 73 optimal weight:    8.9990
   chunk 23 optimal weight:    0.0670
   chunk 25 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9990
   chunk 19 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.5898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   1 GLN
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.083998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.055910 restraints weight = 78052.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.059634 restraints weight = 24094.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.061860 restraints weight = 12476.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.063202 restraints weight = 8217.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.064007 restraints weight = 6297.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8213  Z= 0.123
  Angle     :  0.715  10.775  11203  Z= 0.356
  Chirality :  0.045   0.196   1262
  Planarity :  0.005   0.058   1425
  Dihedral  :  5.583  59.451   1210
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.00 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.21 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.27), residues: 1030
  helix: -1.90 (0.55), residues: 64
  sheet: -0.54 (0.28), residues: 380
  loop : -1.41 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  98 
 TYR   0.021   0.001   TYR C  35 
 PHE   0.029   0.002   PHE E 497 
 TRP   0.018   0.002   TRP B 161 
 HIS   0.004   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8199)
  covalent geometry    : angle       0.71206 (11171)
  SS BOND              : bond        0.00443 (   10)
  SS BOND              : angle       1.14021 (   20)
  hydrogen bonds       : bond        0.02884 (  205)
  hydrogen bonds       : angle       6.36340 (  531)
  link_ALPHA1-6        : bond        0.00754 (    1)
  link_ALPHA1-6        : angle       1.25781 (    3)
  link_BETA1-4         : bond        0.00635 (    2)
  link_BETA1-4         : angle       1.86434 (    6)
  link_NAG-ASN         : bond        0.00306 (    1)
  link_NAG-ASN         : angle       1.15079 (    3)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  338 PHE cc_start: 0.9135 (m-80) cc_final: 0.8844 (m-80)
REVERT: E  406 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8648 (mp0)
REVERT: E  465 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7528 (tt0)
REVERT: E  468 ILE cc_start: 0.9309 (pt) cc_final: 0.9069 (tp)
REVERT: D   18 ARG cc_start: 0.8317 (ttp80) cc_final: 0.8027 (ttp80)
REVERT: D   93 ASN cc_start: 0.8670 (m-40) cc_final: 0.8347 (t0)
REVERT: D  105 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7711 (mp0)
REVERT: D  142 ARG cc_start: 0.8576 (tmt170) cc_final: 0.8043 (ttp80)
REVERT: D  187 GLU cc_start: 0.9529 (tp30) cc_final: 0.9263 (pt0)
REVERT: B  199 GLN cc_start: 0.8423 (mt0) cc_final: 0.8080 (tm-30)
REVERT: B  216 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8123 (ttpp)
REVERT: C  129 PHE cc_start: 0.8251 (m-10) cc_final: 0.8009 (m-10)
REVERT: C  147 CYS cc_start: 0.7781 (p) cc_final: 0.6785 (m)
REVERT: A   38 TYR cc_start: 0.7659 (m-80) cc_final: 0.7316 (m-80)
REVERT: A   49 MET cc_start: 0.8344 (mmm) cc_final: 0.7778 (mmm)
  outliers start: 19
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1014
  time to fit residues: 14.6087
Evaluate side-chains
  108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain E residue  515 PHE
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 80 optimal weight:    0.5980
   chunk 84 optimal weight:    7.9990
   overall best weight:    1.8786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.082451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.054701 restraints weight = 66720.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.058110 restraints weight = 22823.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.060195 restraints weight = 12322.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.061404 restraints weight = 8323.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 69)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.062187 restraints weight = 6531.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3295
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3295
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8213  Z= 0.156
  Angle     :  0.707  10.484  11203  Z= 0.354
  Chirality :  0.044   0.185   1262
  Planarity :  0.005   0.079   1425
  Dihedral  :  5.592  59.648   1210
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.45 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 21.89 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.27), residues: 1030
  helix: -1.68 (0.57), residues: 63
  sheet: -0.62 (0.28), residues: 384
  loop : -1.35 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  98 
 TYR   0.020   0.002   TYR E 495 
 PHE   0.036   0.002   PHE E 497 
 TRP   0.015   0.002   TRP A 152 
 HIS   0.003   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 8199)
  covalent geometry    : angle       0.70381 (11171)
  SS BOND              : bond        0.00410 (   10)
  SS BOND              : angle       1.14472 (   20)
  hydrogen bonds       : bond        0.02985 (  205)
  hydrogen bonds       : angle       6.30435 (  531)
  link_ALPHA1-6        : bond        0.00779 (    1)
  link_ALPHA1-6        : angle       1.15546 (    3)
  link_BETA1-4         : bond        0.00627 (    2)
  link_BETA1-4         : angle       2.07999 (    6)
  link_NAG-ASN         : bond        0.00001 (    1)
  link_NAG-ASN         : angle       1.54503 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2270.93 seconds
wall clock time: 39 minutes 41.58 seconds (2381.58 seconds total)